Genomics and metagenomics in medical microbiology

•Genomics propelled clinical microbiology diagnosis from an empirical to a rational era.•High-throughput genomic sequencing has many applications in clinical microbiology.•Genomics helped deciphering the origin of major infectious outbreaks.•Metagenomics disclosed unexpected relationships between human flora and diseases.

Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.